Org-Babel Ipython and Elpy Conflict


If you use elpy and ob-ipython together and use the jupyter option when configuring the elpy interpreter settings it will break the execution of ob-ipython code blocks, so use the ipython version instead. In other words use this in your init.el file:

(setq python-shell-interpreter "ipython"
      python-shell-interpreter-args "-i --simple-prompt")


I've become quite reliant on ob-ipython for emacs (it lets you use ipython with org-babel to create literate programming documents). I used to use pweave, and if I weren't an emacs user I probably would still use it, and of course there's jupyter notebooks, and the attendant emacs-ipython-notebook that I've used as well (and sometimes still use - as when I need to hand in a Coursera assignment, for instance), but org-mode and ipython seems to hit the sweet spot for me (at least this week).

So I was more than a little disturbed when I tried to execute a code block on my new laptop and found that nothing would run. This is a description of what happened and the fix, in case I forget the next time.

The Problem

I tried executing some python code in an ipython code block but I kept getting an error. This is a toy example of what an ob-ipython block looks like:

#+BEGIN_SRC ipython :session test :results output

To execute it you'd put your cursor somewhere in the block and enter Control-c Control-c.

This is the error I was getting:

There was a fatal error trying to process the request. See *ob-ipython-debug*

And in the *ob-ipython-debug* buffer would be this:

Error executing Jupyter command '/home/dogen/.emacs.d/elpa/ob-ipython-20180113.929/': [Errno 2] No such file or directory

I tried googling for the error, which brought up some Jupyter questions on Stack Overflow that didn't seem relevant. There were also some issues on the ob-ipython github site, but none of them looked exactly the same. They seemed to suggest that the wrong python interpreter was being used, but when I brought up the interpreter in emacs (C-c C-v C-z) it showed the correct interpreter version and I could import the jupyter moduleā€¦ but since that was what people said was the problem and I was using a virtualenv I decided to try setting up pyenv, which apparently lets you switch between python versions fairly easily.

So, I jumped on my desktop to test it out (I ran into the org-mode problem on my laptop, but I was home so I figured I'd switch), but first I brought up emacs and tried executing the same code-block that failed on my laptop, and of course it ran perfectly. So then I went into a long death-spiral of trying to download the ob-ipython git repository and going back in the git-history to see if I could find the place where it might work (my desktop version of ob-ipython was from October of 2017, my laptop's version is from January 2018), and of course none of them worked. Then I tried copying my init.el file from my desktop to my laptop, and suddenly things worked - so it was a configuration problem, but what was it?

The Fix

If you go to the elpy documentation (elpy is a mode for emacs that makes editing python much easier), there is a section on setting up which interpreter to use - and if you're wondering why I'm suddenly talking about elpy instead of ob-ipython, well, it's because it was the problem (or at least using them together was the problem).

The documentation gives you three options for setting the interpreter - python, ipython, or jupyter. This is what my laptop had:

(setq python-shell-interpreter "jupyter"
      python-shell-interpreter-args "console --simple-prompt")

This is what my desktop had:

(setq python-shell-interpreter "ipython"
      python-shell-interpreter-args "-i --simple-prompt")

I don't know why I configured them differently, but I tried using the ipython setting instead of the jupyter setting and all of a sudden - it worked. Maybe I've now broken something else, but it's fixed for now.

#+BEGIN_SRC ipython :session test :results output

: tester


This documents a problem that I ran into wherein the elpy settings I used broke the execution of code blocks by ob-ipython . Just remember to use ipython instead of jupyter and it should be okay. Another day of my life lost to troubleshooting (well, not a whole day, but too much).